Genome data mining of a novel Stutzerimonas marianensis strain LB-0542 isolated from pelagic Sargassum seaweed waste for plastic-degrading and plant growth-promoting traits

TL;DR

A new Stutzerimonas marianensis strain was found to degrade plastics and promote plant growth, based on its genome analysis.

Contribution

The study presents a novel Stutzerimonas marianensis strain with potential for plastic degradation and plant growth promotion, supported by genome data.

Findings

The strain LB-0542 has 34 genes potentially involved in degrading 14 types of plastics.

It contains 3175 genes linked to plant growth-promoting traits like stress control and biofertilization.

The genome has a high GC content (63.2%) and includes 230 CAZyme genes for carbohydrate activity.

Abstract

This study reports the whole-genome sequence data and functional annotations of a novel Stutzerimonas marianensis strain LB-0542 isolated from the decomposing pelagic Sargassum biomass stranded on Long Beach, Barbados. The genomic DNA was sequenced with the Illumina NextSeq2000 platform. The genome assembly was performed with the SPAdes Genome Assembler (ver 3.15.5). The assembled genome has a size of 4520,813 bp, a coverage of 110X, a GC content of 63.2 %, a L50 of 2 and a N50 of 1079,143 bp. The genome consists of 12 contigs, 0 CRISPR, 3 rRNA, 56 tRNA and 4166 CDSs (coding sequences) with a coding ratio of 89.4 %. The genome annotation results for the COG (cluster of orthologous genes) and subsystem features indicate that the metabolism and the amino acids and derivatives are the most dominant categories, respectively. The analysis of the genome for the existence of Carbohydrate-Active Enzymes (CAZymes) identified 230 genes encoding four functional classes of CAZymes [glycoside hydrolases (75 genes), glycosyltransferases (95 genes), carbohydrate esterases (9 genes) and carbohydrate-binding modules (51 genes)]. The functional annotation of the genome for plastic degradation revealed the presence of 34 genes, which could catalyse the degradation process of 14 types of plastics, polyethylene glycol [PEG (29 %)], polylactic acid [PLA (11 %)], poly(3-hydroxybutyrate-co-3-hydroxyvalerate) [PHBV (9 %)], polyhydroxyalkanoates [PHA (9 %)], polyethylene [PE (6 %)], polycaprolactone [PCL (6 %)], polyethersulfone [PES (6 %)], polyethylene terephthalate [PET (6 %)], poly(butylene adipate-co-terephthalate [PBAT (3 %)], (polystyrene [PS (3 %)], polybutylene succinate [PBSA (3 %)], poly(3-hydroxyvalerate) [P3HV (3 %)], polyvinyl alcohol [PVA (3 %)] and natural rubber [NR (3 %)]. The genome mining for plant growth-promoting traits identified 3175 genes that are associated with the colonizing plant system (26 %), competitive exclusion (21 %), stress control (21 %), biofertilization (14 %), phytohormone and plant signal production (10 %), bioremediation (7 %) and plant immune response stimulation (1 %). These genome mining results are an indication of the biotechnological and ecological significance of the novel strain LB-0542 for sustainable biocatalytic processing of Sargassum and plastic-containing waste. The genome sequence data is available in DDBJ/EMBL/GenBank with the accession number BAAIAE000000000.

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